Historic Urban Plans, Inc.
http://www.historicurbanplans.com/
Source for reprints of historic maps. Click on the "Catalog" and the various New York sections
Here is one of my favorites: http://www.historicurbanplans.com/p.tpl?id=350#350

Published by Jeffreys and Faden in 1776, this plan shows the city as surveyed by Bernard Ratzer 1766-1767.

David Rumsey Map Collection
This is a beauty! "original strams, water bodies and wetlands of Manhattan. There is a zoomable online version, but they only sell framed versions...
Sanitary & Topographical Map of the City and Island of New York.
Viele, Egbert L. 1865
http://www.davidrumsey.com/maps6128.html

The Library of Congress' American Memories Map Collection:
Lots of downloadable zoomable images with great resolution! Some beatiful panoramic images.
http://memory.loc.gov/ammem/gmdhtml/gmdhome.html

The New York Public Library
American Shores: Maps of the Middle Atlantic Region to 1850
http://www.nypl.org/research/midatlantic/index.html

University of New Hampshire DIMOND LIBRARY
Documents Department & Data Center
Historic USGS Maps of New England & New York
http://docs.unh.edu/nhtopos/nhtopos.htm

Harlem, NY-NJ Quadrangle 1891, 1897, 1900
USGS 15 Minute Series
http://docs.unh.edu/nhtopos/Harlem.htm

Brooklyn, NY Quadrangle 1891, 1898
USGS 15 Minute Series
http://docs.unh.edu/nhtopos/Brooklyn.htm

Other Resources:

Student Maping Projects:
Green Maps: http://www.greenmap.org/
ERAshop's Newtown Creek Map http://greenapplemap.org/page/sep-erashop
The East River Apprenticeshop (http://www.erashop.org/) is a year-round program teaching leadership and conservation to NYC youth through boat building and seamanship. During the summer of 2003, participants created the Newtown Creek Map.

Aerial Photographs of the Bronx River (and the rest of the US)
At Microsoft's TerraServer

United States Geological Survey
Maps on Demand for New York.
http://store.usgs.gov/mod/ny.html

Some East River History:
http://www.eastrivernyc.org/index.shtml

USGS Water Cycle Poster Multiple Languages
http://ga.water.usgs.gov/edu/watercycle.html